13-72198272-T-C

Variant names:

• chr13-72198272-T-C
• rs471578

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.312 in 151,950 control chromosomes in the GnomAD database, including 9,281 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (9281 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47392 AN: 151832 Hom.: 9258 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.304

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.312 AC: 47450 AN: 151950 Hom.: 9281 Cov.: 31 AF XY: 0.318 AC XY: 23636 AN XY: 74278

African (AFR) AF: 0.492 AC: 20377 AN: 41418

American (AMR) AF: 0.359 AC: 5479 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3590 AN: 5142

South Asian (SAS) AF: 0.260 AC: 1250 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2289 AN: 10566

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12965 AN: 67976

Other (OTH) AF: 0.303 AC: 639 AN: 2110

Alfa AF: 0.262 Hom.: 761

Bravo AF: 0.336

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs471578; hg19: chr13-72772410;